Revealing biological modules via graph summarization

Navlakha, S., Schatz, M. C., Kingsford, C. (2009) Revealing biological modules via graph summarization. Journal of Computational Biology, 16 (2). pp. 253-264. ISSN 10665277 (ISSN)

URL: http://www.ncbi.nlm.nih.gov/pubmed/19183002
DOI: 10.1089/cmb.2008.11TT

Abstract

The division of a protein interaction network into biologically meaningful modules can aid with automated detection of protein complexes and prediction of biological processes and can uncover the global organization of the cell. We propose the use of a graph summarization (GS) technique, based on graph compression, to cluster protein interaction graphs into biologically relevant modules. The method is motivated by defining a biological module as a set of proteins that have similar sets of interaction partners. We show this definition, put into practice by a GS algorithm, reveals modules that are more biologically enriched than those found by other methods. We also apply GS to predict complex memberships, biological processes, and co-complexed pairs and show that in most settings GS is preferable over existing methods of protein interaction graph clustering. © Mary Ann Liebert, Inc. 2009.

Item Type: Paper
Uncontrolled Keywords: Function prediction Graph summarization Module detection Protein interaction networks algorithm article complex formation priority journal protein interaction Algorithms Cluster Analysis Computational Biology Computer Graphics Computer Simulation Databases, Protein Models, Biological Protein Interaction Mapping
Subjects: bioinformatics
bioinformatics > computational biology
CSHL Authors:
Communities: CSHL labs > Schatz lab
Depositing User: Matt Covey
Date: 2009
Date Deposited: 15 Mar 2013 17:53
Last Modified: 15 Mar 2013 17:53
Related URLs:
URI: http://repository.cshl.edu/id/eprint/27835

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